Ontology description
(rdf:type owl:Ontology ) | |
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dcterms:license | http://creativecommons.org/publicdomain/zero/1.0/ |
spin:imports | http://topbraid.org/spin/owlrl-all |
spin:imports | http://topbraid.org/spin/rdfsplus |
spin:imports | http://topbraid.org/spin/spinowl |
owl:versionInfo | "Created at the DBCLS RDF Summit 2, Sendai Japan 20" xsd:string |
Classes
vg:GAMP_Format (rdf:type owl:Class ) | |
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rdfs:comment | Contains a DAG of subalignments to different paths through the reference graph |
rdfs:isDefinedBy | https://raw.githubusercontent.com/vgteam/vg/master/src/vg.proto |
rdfs:label | MultipathAlignment |
vg:GAM_Format (rdf:type owl:Class ) | |
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rdfs:comment | Contains an alignment to a graph |
rdfs:isDefinedBy | https://raw.githubusercontent.com/vgteam/vg/master/src/vg.proto |
rdfs:label | Alignment |
rdfs:subClassOf | http://edamontology.org/format_2055 |
vg:GBWT_Format (rdf:type owl:Class ) | |
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rdfs:comment | Graph Burrows-Wheeler Transform, a succinct collection of paths through a genome graph, published by Jouni Siren. Usually represents haplotypes. |
rdfs:isDefinedBy | https://raw.githubusercontent.com/vgteam/vg/master/src/vg.proto |
rdfs:label | GBWT |
vg:GCSA2_Format (rdf:type owl:Class ) | |
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rdfs:comment | Generalized compressed suffix array 2, an exact match index published by Jouni Siren |
rdfs:isDefinedBy | https://raw.githubusercontent.com/vgteam/vg/master/src/vg.proto |
rdfs:label | GCSA2 |
vg:Node (rdf:type owl:Class ) | |
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rdfs:comment | "A node in the variant graph, representing a sequence section." xsd:string |
rdfs:label | "Node" xsd:string |
rdfs:subClassOf | owl:Thing |
vg:Path (rdf:type owl:Class ) | |
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rdfs:comment | "A Path is a collection of steps from path to path that represent an asserdfs:labelmbled sequence integrated into the variant grap." xsd:string |
rdfs:label | "Path" xsd:string |
rdfs:subClassOf | owl:Thing |
vg:Snarl_Format (rdf:type owl:Class ) | |
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rdfs:comment | A series of Snarl objects, each of which contain: The boundaries of a snarl (a bubble-like motif in a graph), the snarl (if any) that contains this one, classifications of the snarl based on the reachability of the two boundary nodes from each other and the cyclic-ness of the subcomponent. |
rdfs:isDefinedBy | https://raw.githubusercontent.com/vgteam/vg/master/src/vg.proto |
rdfs:label | Snarl |
vg:Snarl_Traversal_Format (rdf:type owl:Class ) | |
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rdfs:comment | A series of SnarlTraversal objects, each of which contain: A walk in the graph through a Snarl, and optionally a name. |
rdfs:isDefinedBy | https://raw.githubusercontent.com/vgteam/vg/master/src/vg.proto |
rdfs:label | SnarlTraversal |
vg:Step (rdf:type owl:Class ) | |
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rdfs:comment | "A step along a path in the variant graph. A series of steps along a path represent an assembled sequence that was originally inserted into the the variant graph. A step points to a :Node or the reverse complement of a node and has a rank (step number)." xsd:string |
rdfs:label | "Step" xsd:string |
rdfs:subClassOf | owl:Thing |
vg:VG_Format (rdf:type owl:Class ) | |
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rdfs:comment | Consists of nodes, edges, and paths. Nodes each have a unique ID and a DNA sequence, edges consist of two node sides (so the graph is bidirected), and paths are a sequence of nodes and orientations. Paths also have names. |
rdfs:isDefinedBy | https://raw.githubusercontent.com/vgteam/vg/master/src/vg.proto |
rdfs:label | Graph |
rdfs:subClassOf | http://edamontology.org/format_2055 |
rdfs:subClassOf | http://edamontology.org/format_2921 |
vg:XG_Format (rdf:type owl:Class ) | |
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rdfs:comment | An immutable, succinct representation of a graph. Contains the same info as the .vg. |
rdfs:isDefinedBy | https://raw.githubusercontent.com/vgteam/vg/master/src/vg.proto |
rdfs:label | XG |
rdfs:seeAlso | vg:VG_Format |
Properties
Object properties
vg:links (rdf:type owl:ObjectProperty ) | |
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rdfs:comment | "The super property that says two nodes are linked and does not allow one to infer wwhich side to side it goes" xsd:string |
rdfs:domain | vg:Node |
rdfs:label | "links" xsd:string |
rdfs:range | vg:Node |
vg:linksForwardToForward (rdf:type owl:ObjectProperty ) | |
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rdfs:comment | "This links a node from the forward (5' to 3') strand on the subject node to the forward (5' to 3') strand on the predicate node." xsd:string |
rdfs:domain | vg:Node |
rdfs:label | "++" xsd:string |
rdfs:label | "linksForwardToForward" xsd:string |
rdfs:range | vg:Node |
rdfs:subPropertyOf | vg:links |
vg:linksForwardToReverse (rdf:type owl:ObjectProperty ) | |
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rdfs:comment | "This links a node from the forward (5' to 3') strand on the subject node to the reverse (3' to 5') strand on the predicate node." xsd:string |
rdfs:domain | vg:Node |
rdfs:label | "+-" xsd:string |
rdfs:label | "linksForwardToReverse" xsd:string |
rdfs:range | vg:Node |
rdfs:subPropertyOf | vg:links |
vg:linksReverseToForward (rdf:type owl:ObjectProperty ) | |
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rdfs:comment | "This links a node from the reverse (3' to 5') strand on the subject node to the forward (5' to 3') strand on the predicate node." xsd:string |
rdfs:domain | vg:Node |
rdfs:label | "-+" xsd:string |
rdfs:label | "linksReverseToForward" xsd:string |
rdfs:range | vg:Node |
rdfs:subPropertyOf | vg:links |
vg:linksReverseToReverse (rdf:type owl:ObjectProperty ) | |
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rdfs:comment | "This links a node from the reverse (3' to 5') strand on the subject node to the reverse (3' to 5') strand on the predicate node." xsd:string |
rdfs:domain | vg:Node |
rdfs:label | "--" xsd:string |
rdfs:label | "linksReverseToReverse" xsd:string |
rdfs:range | vg:Node |
rdfs:subPropertyOf | vg:links |
vg:node (rdf:type owl:ObjectProperty ) | |
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rdfs:comment | "This means that this step occurs on the forward strand of the sequence attaced to the node (i.e. it is on the explicit encoded forward (5' to 3') strand) of the predicate node." xsd:string |
rdfs:domain | vg:Step |
rdfs:label | "node" xsd:string |
rdfs:range | vg:Node |
vg:path (rdf:type owl:ObjectProperty ) | |
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rdfs:comment | "This means that this step occurs on the path that is the object of this statment" xsd:string |
rdfs:domain | vg:Step |
rdfs:label | "path" xsd:string |
rdfs:range | vg:Path |
vg:position (rdf:type owl:ObjectProperty ) | |
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rdfs:comment | "This is the position on the reference path at which this step starts." xsd:string |
rdfs:domain | vg:Step |
rdfs:label | "position" xsd:string |
rdfs:range | xsd:positiveInteger |
vg:reverseOfNode (rdf:type owl:ObjectProperty ) | |
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rdfs:comment | "This means this step occurs on the revese complement of the sequence attaced to the node (i.e. it is on the implicit reverse (3' to 5') strand) of the predicate node." xsd:string |
rdfs:domain | vg:Step |
rdfs:label | "reverseOfNode" xsd:string |
rdfs:range | vg:Node |
Datatype properties
vg:rank (rdf:type owl:DatatypeProperty ) | |
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rdfs:comment | "The rank records the step place along its path." xsd:string |
rdfs:domain | vg:Step |
rdfs:label | "rank" xsd:string |
rdfs:range | xsd:positiveInteger |